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Protein domain assignment from the recurrence of locally similar structures
Author(s) -
Tai ChinHsien,
Sam Vichetra,
Gibrat JeanFrancois,
Garnier Jean,
Munson Peter J.,
Lee Byungkook
Publication year - 2011
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22923
Subject(s) - structural genomics , protein data bank (rcsb pdb) , domain (mathematical analysis) , protein domain , protein structure , structural classification of proteins database , protein data bank , computer science , protein structure database , structural alignment , computational biology , protein structure prediction , structural bioinformatics , protein secondary structure , crystallography , sequence alignment , biology , mathematics , chemistry , genetics , peptide sequence , gene , biochemistry , sequence database , mathematical analysis
Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra‐domain versus inter‐domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one‐against‐all structure comparisons with a dataset of 6373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies. Proteins 2011. Published 2010 Wiley‐Liss, Inc.